public void ChromatogramTest()
{
Chromatogram a = new Chromatogram(new double[] { 1, 2, 3, 4, 5 }, new double[] { 1, 2, 6, 4, 2 }, false);
var b = a.CreateSmoothChromatogram(SmoothingType.BoxCar, 4);
Assert.IsTrue(b.GetTimes().SequenceEqual(new double[] { 2, 3, 4 }));
Assert.IsTrue(b.GetIntensities().SequenceEqual(new double[] { 3, 4, 4 }));
Chromatogram d = new Chromatogram(new double[] { 1, 2, 3, 4, 5, 6, 7, 8, 9 }, new double[] { 10, 0, 2, 6, 2, 0, 1, 10, 1 }, false);
// Finds the APEX! Not nearest peak!
Assert.AreEqual(6, d.FindNearestApex(5.9, 1).Intensity);
Assert.AreEqual(10, d.FindNearestApex(6.1, 1).Intensity);
var elutionProfile = d.GetElutionProfile(new DoubleRange(3, 7));
Assert.AreEqual(5, elutionProfile.Count);
Assert.AreEqual(9.5, elutionProfile.TrapezoidalArea());
Assert.AreEqual(2, elutionProfile.StartPeak.Intensity);
Assert.AreEqual(3, elutionProfile.StartPeak.Time);
Assert.AreEqual(7, elutionProfile.EndPeak.Time);
var thePeak = new ChromatographicPeak(1, 10);
Assert.AreEqual(1, thePeak.Time);
Assert.AreEqual(10, thePeak.Intensity);
Assert.AreEqual("(1, 10)", thePeak.ToString());
var elutionProfileEmpty = d.GetElutionProfile(new DoubleRange(6.5, 6.5));
Assert.AreEqual(0, elutionProfileEmpty.TrapezoidalArea());
Assert.AreEqual(0, elutionProfileEmpty.SummedArea);
Assert.AreEqual("Count = 9 TIC = 32", d.ToString());
Assert.AreEqual(10, d.GetApex().Intensity);
Assert.AreEqual(1, d.GetApex().Time);
}
public int CompareTo(ChromatographicPeak other)
{
return(Time.CompareTo(other.Time));
}
//This function changes the LFQ (apex) intensities of the peaks to be SILAC intensities that only use intensities from MS1 scans where both heavy and light were quantified (only requires 2 for missed cleavages)
//TODO: unclear how this affects data quality when deuterium shift is in play. A retention time calibration may be necessary.
private static void CalculateSilacIntensities(Dictionary <SpectraFileInfo, List <ChromatographicPeak> > peakDictionary, Dictionary <string, List <FlashLFQ.Peptide> > unlabeledToPeptidesDictionary)
{
foreach (KeyValuePair <SpectraFileInfo, List <ChromatographicPeak> > kvp in peakDictionary)
{
//make a dictionary for easy peak lookup from peptide sequences
Dictionary <string, ChromatographicPeak> sequenceToPeakDictionary = new Dictionary <string, ChromatographicPeak>();
foreach (ChromatographicPeak peak in kvp.Value)
{
//sometimes chromatographic peaks are separated (elute on both sides of the gradient, random blips, etc)
//in these situations, we want to use both chromatographic peaks for quantification, not just a single one.
string fullSequence = peak.Identifications.First().ModifiedSequence;
if (sequenceToPeakDictionary.ContainsKey(fullSequence))
{
ChromatographicPeak previousPeak = sequenceToPeakDictionary[fullSequence];
previousPeak.IsotopicEnvelopes.AddRange(peak.IsotopicEnvelopes);
}
else
{
sequenceToPeakDictionary.Add(fullSequence, peak);
}
}
foreach (List <FlashLFQ.Peptide> peptideGroup in unlabeledToPeptidesDictionary.Select(x => x.Value))
{
List <string> sequences = peptideGroup.Select(x => x.Sequence).ToList();
//get peaks of interest for this peptide group
List <ChromatographicPeak> peaksOfInterest = new List <ChromatographicPeak>();
foreach (string sequence in sequences)
{
if (sequenceToPeakDictionary.TryGetValue(sequence, out ChromatographicPeak peakOfInterest))
{
peaksOfInterest.Add(peakOfInterest);
}
}
//If there are fewer than 2 peaks, we can't do any comparisons
if (peaksOfInterest.Count > 1)
{
//get isotopic envelopes that are shared by all
List <int> scanIndex = peaksOfInterest.First().IsotopicEnvelopes.Select(x => x.IndexedPeak).Select(x => x.ZeroBasedMs1ScanIndex).ToList();
for (int i = 1; i < peaksOfInterest.Count; i++)
{
List <int> currentScanIndexes = peaksOfInterest[i].IsotopicEnvelopes.Select(x => x.IndexedPeak).Select(x => x.ZeroBasedMs1ScanIndex).ToList();
scanIndex = scanIndex.Intersect(currentScanIndexes).ToList();
if (scanIndex.Count == 0) //if there's no overlap, then we're done!
{
break;
}
}
//if we aren't sticking with the default values
if (scanIndex.Count != 0)
{
//update peptides
foreach (FlashLFQ.Peptide peptide in peptideGroup)
{
ChromatographicPeak peakForThisPeptide = peaksOfInterest.Where(x => peptide.Sequence.Equals(x.Identifications.First().ModifiedSequence)).FirstOrDefault();
if (peakForThisPeptide != null)
{
double summedIntensity = peakForThisPeptide.IsotopicEnvelopes.Where(x => scanIndex.Contains(x.IndexedPeak.ZeroBasedMs1ScanIndex)).Select(x => x.Intensity).Sum();
peptide.SetIntensity(kvp.Key, summedIntensity);
}
else //rare instance, cause unknown. Crash identified using 180524_LMuscle_30d_bio3.raw, Mus_Canonical_180122.xml, 1 missed cleavage
{
peptide.SetIntensity(kvp.Key, 0);
}
}
}
}
}
}
}
public int CompareTo(ChromatographicPeak other)
{
return Time.CompareTo(other.Time);
}
